Sat Oct 15 11:26:06 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 11:26:06 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3286 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5976765 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 51.60600 111.1700 ymin,ymax (A): -18.89500 40.56100 zmin,zma (A): -34.33900 24.43900 x,y,z range (A): 59.56400 59.45600 58.77800 scale (grids/A): 0.5976765 object centre (A): 81.38800 10.83300 -4.950001 number of atom coordinates read : 3286 total number of charged atoms : 3145 net assigned charge : 4.000026 assigned positive charge : 488.5426 centred at (gu) : 88.05870 89.59211 91.75639 assigned negative charge : -484.5439 centred at (gu) : 88.05456 89.72458 91.76156 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7959 nv = 96 ne = 84 npr = 65673 no. pairs analyzed = 65673 no. exposed pairs = 4338 no. arc points = 30429 no. surface atoms = 1440 nbur = 1846 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 372 mr = 4141 m= 0 mr = 26 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.2300000 number of dielectric boundary points 4164 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3075 ## 288 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9885 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2102729E-09 1.9799069E-09 midg,1,midg; midg,igrid,midg 7.7379321E-09 -3.7172772E-09 1,midg,midg; igrid,midg,midg 2.1316158E-09 1.1350627E-09 gauss-seidel spectral radius is 0.9855778 estimated iterations to convergence 68 setup time was (sec) 0.4700000 now iterating at: 11:26:07 rms-change max change #iterations 0.1210586 17.13585 at 10iterations 1.1598977E-02 1.607422 at 20iterations 2.1109446E-03 0.3511848 at 30iterations 6.8169844E-04 0.1139832 at 40iterations 2.3674661E-04 3.9646149E-02 at 50iterations finished qdiffx linear iterations at : 11:26:10 total time elapsed so far: 3.830000 # loops : 50 mean,max change (kT/e) : 2.3674661E-04 3.9646149E-02 energy calculations done at 3.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.970000 DelPhi exited at 11:26:10 3.974u 0.245s 0:04.56 92.3% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 11:26:10 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3286 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.793029 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 51.60600 111.1700 ymin,ymax (A): -18.89500 40.56100 zmin,zma (A): -34.33900 24.43900 x,y,z range (A): 59.56400 59.45600 58.77800 scale (grids/A): 1.793029 object centre (A): 81.38800 10.83300 -4.950001 number of atom coordinates read : 3286 total number of charged atoms : 3145 net assigned charge : 4.000026 assigned positive charge : 488.5426 centred at (gu) : 84.17544 88.77509 95.26852 assigned negative charge : -484.5439 centred at (gu) : 84.16328 89.17319 95.28426 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 85808 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30429 grid for indexing accessible points = 1.400000 m= 29358 mr = 58027 m= 4094 mr = 20692 m= 177 mr = 2410 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 2607 time to turn everything in is 0.4300000 number of dielectric boundary points 38268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 226 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 24560 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5976765 object centre at (A) : 81.38800 10.83300 -4.950001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1134759E-02 2.2674121E-02 midg,1,midg; midg,igrid,midg 1.8769568E-02 -2.8537473E-02 1,midg,midg; igrid,midg,midg 1.1850120E-02 1.9860440E-03 gauss-seidel spectral radius is 0.9985340 estimated iterations to convergence 207 setup time was (sec) 0.6500000 now iterating at: 11:26:11 rms-change max change #iterations 4.254816 168.1694 at 10iterations 1.923938 65.76511 at 20iterations 0.8757688 31.24747 at 30iterations 0.3991863 12.53949 at 40iterations 0.1818992 5.372053 at 50iterations 8.2804471E-02 2.506558 at 60iterations 3.7974305E-02 1.177647 at 70iterations 1.7617472E-02 0.5381365 at 80iterations 8.2666175E-03 0.2508354 at 90iterations 4.0305275E-03 0.1275635 at 100iterations 2.0808836E-03 7.4897766E-02 at 110iterations 1.1507099E-03 3.8917542E-02 at 120iterations finished qdiffx linear iterations at : 11:26:20 total time elapsed so far: 8.540000 # loops : 120 mean,max change (kT/e) : 1.1507099E-03 3.8917542E-02 energy calculations done at 8.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.670000 DelPhi exited at 11:26:21 8.676u 0.223s 0:10.46 84.9% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 11:26:21 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3286 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.689544 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 51.60600 111.1700 ymin,ymax (A): -18.89500 40.56100 zmin,zma (A): -34.33900 24.43900 x,y,z range (A): 59.56400 59.45600 58.77800 scale (grids/A): 2.689544 object centre (A): 81.38800 10.83300 -4.950001 number of atom coordinates read : 3286 total number of charged atoms : 3145 net assigned charge : 4.000026 assigned positive charge : 488.5426 centred at (gu) : 81.26282 88.16242 97.90240 assigned negative charge : -484.5439 centred at (gu) : 81.24470 88.75964 97.92641 start vw surface at 0.1000000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 198680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30429 grid for indexing accessible points = 1.400000 m= 96574 mr = 141320 m= 32804 mr = 77034 m= 7036 mr = 25515 m= 803 mr = 5168 m= 27 mr = 475 m= 0 mr = 2 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 9101 time to turn everything in is 1.110000 number of dielectric boundary points 86410 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 25150 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.793029 object centre at (A) : 81.38800 10.83300 -4.950001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1378383 0.1899274 midg,1,midg; midg,igrid,midg 0.2429038 -0.3377936 1,midg,midg; igrid,midg,midg 0.4811065 -2.6457975E-02 gauss-seidel spectral radius is 0.9992498 estimated iterations to convergence 288 setup time was (sec) 1.410000 now iterating at: 11:26:23 rms-change max change #iterations 10.59895 389.1913 at 10iterations 6.326260 165.8660 at 20iterations 3.722472 80.58679 at 30iterations 2.175862 53.25972 at 40iterations 1.268492 25.14290 at 50iterations 0.7341717 13.86056 at 60iterations 0.4259216 8.112419 at 70iterations 0.2458793 5.395138 at 80iterations 0.1418093 2.599892 at 90iterations 8.1755616E-02 1.448380 at 100iterations 4.7069114E-02 0.8529510 at 110iterations 2.7124446E-02 0.5139847 at 120iterations 1.5639685E-02 0.2775726 at 130iterations 9.0401061E-03 0.1770401 at 140iterations 5.2603795E-03 9.8045349E-02 at 150iterations 3.0961267E-03 5.7579041E-02 at 160iterations 1.8609299E-03 3.4839630E-02 at 170iterations 1.1522300E-03 2.4440765E-02 at 180iterations finished qdiffx linear iterations at : 11:26:39 total time elapsed so far: 15.17000 # loops : 180 mean,max change (kT/e) : 1.1522300E-03 2.4440765E-02 energy calculations done at 15.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.30000 DelPhi exited at 11:26:40 15.297u 0.299s 0:18.67 83.4% 0+0k 0+0io 0pf+0w